What do the B and Y Matches mean?

The BY matches are fragment ions found in the high energy data that suggest a particular identification for a given precursor ion found in the low energy data.

A peptide that is intact in the low energy data should be represented by various products in the high energy data. These products will be formed when the originating peptide is split at a peptide bond between two amino acids. The B and Y ions for a given peptide represent the two halves formed by splitting the original peptide between various amino acids. For a given peptide sequence, the B ions are the product when the charge is retained on the N-Terminus (i.e. at the beginning of the sequence) and the Y ions the product when the charge is retained at the C-Terminus (i.e. at the end of the sequence). For example, for the sequence IQLVEEELDR the b3 and y3 ions correspond to splitting the peptide after the third amino acid: b3 = IQL and y3 RDLEEEV (Y ions are written in reverse order). Product ions with a neutral loss are annotated with a degree symbol (°) to show water loss or an asterisk (*) to denote loss of an ammonia.

The full list of all products that correspond to a given identification are shown in the BY Matches column in the table, so b2b4b4*y3y3° means that the evidence for this identification is b2, b4, b4 with ammonia loss, y3 and y3 with water loss. The more fragments found for a given identification the more likely it is to be correct.

The graph below the table can be used to explore the product ions; it shows all the B ions in blue, and Y ions in red, with ions that have a neutral loss shown in green (regardless of whether they are B or Y ions). Hover the mouse over a peak in the graph to get information about which ion it is, its mass and intensity. You can zoom in on the graph by dragging an area with the mouse and zoom out by right-clicking and choosing from the context menu.